Rolf,
You're right. It appears to work in build 11.3.33. I currently have
build 11.2.8 loaded. I will try to upgrade.
Bob, you requested I send you the state so you can look at it. It
appears to be a problem with the older release of Jmol, so perhaps
investigating the state printout is not relevant anymore but anyways
here it is.
# Jmol state version 11.2.8 2007-07-23 12:04;
# window state;
# height 300;
# width 300;
initialize;
stateVersion = 1102008;
refreshing = false;
backgroundColor = "[xffffff]";
axis1Color = "[xff0000]";
axis2Color = "[x008000]";
axis3Color = "[x0000ff]";
ambientPercent = 45;
diffusePercent = 84;
specular = true;
specularPercent = 22;
specularPower = 40;
specularExponent = 6;
# file state;
allowEmbeddedScripts = false;
autoBond = true;
appendNew = true;
applySymmetryToBonds = false;
bondRadiusMilliAngstroms = 150;
bondTolerance = 0.45;
defaultLattice = {0.0 0.0 0.0};
defaultLoadScript = "";
loadFormat = "http://www.rcsb.org/pdb/files/%FILE.pdb";;
forceAutoBond = false;
minBondDistance = 0.4;
percentVdwAtom = 20;
load "http://132.77.150.123/cgi-bin/getpdb.pl?1xjo";;
# settings;
refreshing = false;
defaultanglelabel = "%VALUE %UNITS";
defaultcolorscheme = "Jmol";
defaultdistancelabel = "%VALUE %UNITS";
defaultloadscript = "";
defaulttorsionlabel = "%VALUE %UNITS";
defaulttranslucent = 0.5;
allowembeddedscripts = true;
allowrotateselected = false;
applysymmetrytobonds = false;
autobond = true;
autofps = false;
axes = window;
axesmode = 0;
axesscale = 2.0;
bondmodeor = false;
bondradiusmilliangstroms = 150;
bondtolerance = 0.45;
cartoonrockets = false;
chaincasesensitive = false;
disablepopupmenu = false;
displaycellparameters = true;
dotsselectedonly = false;
dotsurface = true;
dynamicmeasurements = false;
forceautobond = false;
greyscalerendering = false;
hbondsbackbone = false;
hbondssolid = false;
helppath = "http://www.stolaf.edu/academics/chemapps/jmol/docs/
index.htm";
hermitelevel = 0;
hidenameinpopup = false;
hidenavigationpoint = false;
highresolutionflag = false;
hoverdelay = 0.5;
isspinning = true;
justifymeasurements = false;
loadformat = "http://www.rcsb.org/pdb/files/%FILE.pdb";;
measureallmodels = false;
minbonddistance = 0.4;
navigationcentered = false;
navigationperiodic = false;
navigationspeed = 5.0;
percentvdwatom = 20;
perspectivedepth = true;
pickingspinrate = 10;
propertyatomnumberfield = 0;
propertycolorscheme = "roygb";
propertydatafield = 0;
rangeselected = false;
ribbonaspectratio = 16;
ribbonborder = false;
scriptdelay = 0;
selecthetero = true;
selecthydrogen = true;
selectionhalos = false;
sheetsmoothing = 1.0;
showhiddenselectionhalos = false;
showhydrogens = true;
showmeasurements = true;
showmultiplebonds = true;
shownavigationpointalways = false;
solvent = false;
solventproberadius = 1.2;
spinflag = true;
ssbondsbackbone = true;
testflag1 = false;
testflag2 = false;
testflag3 = false;
testflag4 = false;
tracealpha = true;
usenumberlocalization = true;
vectorscale = 1.0;
vibrationperiod = 1.0;
vibrationscale = 1.0;
zoomlarge = true;
zshade = false;
# connections;
calculate hbonds
# label defaults;
select none;
color label none;
background label none;
labelOffset = 4 4;
labelAlignment = left;
labelPointer = off;
font label 13 SansSerif Plain;
# model state;
structure sheet ({0:34}) # model=1 & (1 - 5);
structure helix ({35:157}) # model=1 & (6 - 22);
structure none ({158:222}) # model=1 & (23 - 31);
structure helix ({223:343}) # model=1 & (32 - 47);
structure none ({344:352}) # model=1 & (48 - 49);
structure sheet ({353:429}) # model=1 & (50 - 58);
structure none ({430:443}) # model=1 & (59 - 61);
structure sheet ({444:522}) # model=1 & (62 - 71);
structure none ({523:560}) # model=1 & (72 - 77);
structure sheet ({561:616}) # model=1 & (78 - 85);
structure none ({617:624}) # model=1 & (86 - 86);
structure sheet ({625:645}) # model=1 & (87 - 89);
structure none ({646:702}) # model=1 & (90 - 98);
structure helix ({703:805}) # model=1 & (99 - 114);
structure none ({806:814}) # model=1 & (115 - 116);
structure sheet ({815:842}) # model=1 & (117 - 119);
structure none ({843:850}) # model=1 & (120 - 120);
structure sheet ({851:932}) # model=1 & (121 - 128);
structure none ({933:979}) # model=1 & (129 - 135);
structure helix ({980:1052}) # model=1 & (136 - 144);
structure none ({1053:1067}) # model=1 & (145 - 146);
structure helix ({1068:1112}) # model=1 & (147 - 152);
structure none ({1113:1125}) # model=1 & (153 - 154);
structure sheet ({1126:1168}) # model=1 & (155 - 159);
structure none ({1169:1218}) # model=1 & (160 - 166);
structure sheet ({1219:1271}) # model=1 & (167 - 172);
structure none ({1272:1295}) # model=1 & (173 - 175);
structure helix ({1296:1402}) # model=1 & (176 - 188);
structure none ({1403:1418}) # model=1 & (189 - 190);
structure sheet ({1419:1448}) # model=1 & (191 - 194);
structure none ({1449:1466}) # model=1 & (195 - 203);
structure helix ({1467:1524}) # model=1 & (204 - 210);
structure none ({1525:1535}) # model=1 & (211 - 212);
structure sheet ({1536:1556}) # model=1 & (213 - 215);
structure none ({1557:1560}) # model=1 & (216 - 216);
structure sheet ({1561:1583}) # model=1 & (217 - 219);
structure none ({1584:1603}) # model=1 & (220 - 223);
structure sheet ({1604:1630}) # model=1 & (224 - 227);
structure helix ({1631:1672}) # model=1 & (228 - 233);
structure none ({1673:1852}) # model=1 & (234 - 257);
structure helix ({1853:1994}) # model=1 & (258 - 276);
structure none ({1995:2000}) # model=1 & (277 - 277);
select ({2008});
Spacefill 1.973;
select ({0:1176 1186:2000});
color atoms opaque [xadd8e6];
select ({2001 2002});
Spacefill 1.39;
select ({1184 1185});
Spacefill 1.7;
select ({1177});
Spacefill 1.85;
select ({0:1176 1186:2000});
Spacefill 0.0;
select ({1178:1180 1182 1183});
Spacefill 1.95;
select ({1181});
Spacefill 2.0;
select BONDS ({16});
color bonds opaque [xffff00];
wireframe 0.2;
select BONDS ({5 7:15 26:2232});
wireframe 0.0;
measures = nanometers;
font measures 15 SansSerif Plain;
select measures ({null});
select ({0:2000});
Cartoon on;
boundBox off;
;
unitcell off;
;
frank on;
font frank 16 SansSerif Bold;
# orientation/center/spin state;
set refreshing false;
perspectiveModel = 11;
cameraDepth = 3.0;
center {19.550499 14.5795 45.547005};
moveto /* time, axisAngle */ 0.0 { 0 1000 0 20.17} /* zoom,
translation */ 100.0 0.0 0.0 /* center, rotationRadius */
{19.550499 14.5795 45.547005} 31.976118 /* navigation center,
translation, depth */ {0.0 0.0 0.0} -45.40585 19.49943 50.0;;
slab 100;depth 0;
spinX = 0;spinY = 5;spinZ = 0;spinFps = 30;
refreshing = true;refresh;
spin on;
# selection state;
select ({2009:2257});
hide selected;
select ({0:2257});
refreshing = true;
Best,
Eran
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